THEx

THEx visualizes phylogenomic data alongside genomic annotations to enable chromosome-by-chromosome analysis of evolutionary histories and genetic divergence.

Key Features:

• Phylogenomic–annotation integration: Integrates phylogenomic data with genomic annotations for joint genome-wide analysis.
• Chromosome-level visualization: Visualizes evolutionary histories and genetic divergence on a chromosome-by-chromosome basis.
• Continuous sliding-window comparisons: Performs continuous sliding-window comparisons across chromosomes to assess local evolutionary histories.
• Annotation layers: Incorporates gene annotations, recombination rates, and other user-specified feature annotations.
• Comparative analysis: Supports analysis of genomic variation and evolutionary patterns across species or populations.

Scientific Applications:

• Phylogenomic analysis: Dissect complex evolutionary histories embedded within genomes.
• Genetic divergence examination: Examine genetic divergence across chromosomes.
• Comparative genomics: Compare evolutionary patterns and genomic variation across different species or populations.
• Recombination-aware interpretation: Relate recombination rates and gene annotations to phylogenomic signals.

Methodology:

Chromosome-by-chromosome visualization using continuous sliding-window comparisons that incorporate gene annotations, recombination rates, and other user-specified annotation layers.